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Nucleic Acids Research 2006 34(6):1816-1835; doi:10.1093/nar/gkl085
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Published online 5 April 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications

Christian Marck*, Rym Kachouri-Lafond1, Ingrid Lafontaine2, Eric Westhof1, Bernard Dujon2 and Henri Grosjean3

Service de Biochimie et de Génétique Moléculaire Bât 144. CEA/Saclay, 91191 Gif-sur-Yvette, France 1 Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UPR 9002 ‘Architecture et Réactivité de l‘ARN’, Université Louis Pasteur, 15 rue Descartes, 67084 Strasbourg, France 2 Unité de Génétique Moléculaire des Levures, Institut Pasteur 25 rue du Dr Roux, 75724 Paris, France 3 Laboratoire d'Enzymologie et Biochimie Structurales, Bât 34. Centre National de la Recherche Scientifique 1 av. de la Terrasse, 91198 Gif-sur-Yvette, France

*To whom correspondence should be addressed. Tel: 33 (0)1 69 08 46 20; Fax: 33 (0)1 69 08 47 12; Email: christian.marck{at}cea.fr

Received December 7, 2005. Revised February 3, 2006. Accepted March 3, 2006.

We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic ‘p-distance tree’ using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes.


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